Re: substitution probabilities and distance-based tree-reconstruction
- From: "Malcolm" <regniztar@xxxxxxxxxxxxxx>
- Date: Sat, 24 Sep 2005 18:29:33 -0400 (EDT)
"Daniel" <schuetz-kemmern@xxxxxxxxxxx> wrote
> can I also use substitution probabilities instaed of "real distances"
> by the distance-based reconstruction of phylogenetic trees? How should
> gaps (after aligning) be estimate (which value)?
>
Can you give a bit more information in your posts?
I presume you are talking about phylogenetic trees of proteins.
Divergence of two proteins is an historical event, which could potentially
be located in time. In practise of course we don't have perfect evidence,
and so we assume that two proteins which are very different must have
diverged longer ago than two proteins which are similar.
However some proteins, like histones (which package DNA) are very well
conserved, others, such as the immune system proteins, diverge very rapidly.
Some amino acid substitutions are conservative (the replacement is
chemically similar to the original), some are not.
Some substitutions will be close to an active site, and have an effect on
the activity on an enzyme, some will have little or no effect.
Also, some changes to DNA are more likely than others. Mutations are not
evenly distributed. Usually we say that an insertion or deletion is one of
the less likely mutations, hence the "gap penalty" for aligning proteins is
fairly large. However there is no consensus on exactly how large it should
be.
What this boils down to is that there is no obvious method for trying to
reconstruct the historical timetable, and you may not be interested in
strict chronology anyway - generation time may be what you are looking at.
.
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